diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java index 2676f7067..19dc99682 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerIntegrationTest.java @@ -32,13 +32,6 @@ public class IndelRealignerIntegrationTest extends WalkerTest { 1, Arrays.asList(base_md5_with_SW_or_VCF)); executeTest("test realigner defaults with VCF", spec2); - - WalkerTestSpec spec3 = new WalkerTestSpec( - baseCommand + "-D " + GATKDataLocation + "dbsnp_129_b36.rod", - 1, - Arrays.asList(base_md5)); - executeTest("realigner defaults with dbsnp", spec3); - } @Test @@ -48,12 +41,6 @@ public class IndelRealignerIntegrationTest extends WalkerTest { 1, Arrays.asList("3dd5d2c9931b375455af0bff1a2c4888")); executeTest("realigner known indels only from VCF", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel KNOWNS_ONLY -D " + GATKDataLocation + "dbsnp_129_b36.rod", - 1, - Arrays.asList("05a114623c126b0398fbc1703437461e")); - executeTest("realigner known indels only from dbsnp", spec2); } @Test @@ -63,12 +50,6 @@ public class IndelRealignerIntegrationTest extends WalkerTest { 1, Arrays.asList(base_md5_with_SW_or_VCF)); executeTest("realigner use SW from VCF", spec1); - - WalkerTestSpec spec2 = new WalkerTestSpec( - baseCommand + "--consensusDeterminationModel USE_SW -D " + GATKDataLocation + "dbsnp_129_b36.rod", - 1, - Arrays.asList(base_md5_with_SW_or_VCF)); - executeTest("realigner use SW from dbsnp", spec2); } @Test diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java index fd5ad0b22..e8b5033cf 100755 --- a/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java +++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/indels/IndelRealignerPerformanceTest.java @@ -30,7 +30,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest { " -LOD 5" + " -maxConsensuses 100" + " -greedy 100" + - " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" + + " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" + " -o /dev/null" + " -I " + evaluationDataLocation + "NA12878.GAII.chr1.50MB.bam" + " -L chr1:1-5,650,000" + @@ -45,7 +45,7 @@ public class IndelRealignerPerformanceTest extends WalkerTest { " -LOD 5" + " -maxConsensuses 100" + " -greedy 100" + - " -D /humgen/gsa-hpprojects/GATK/data/dbsnp_129_hg18.rod" + + " -B:dbsnp,vcf " + GATKDataLocation + "dbsnp_132.hg18.vcf" + " -o /dev/null" + " -I " + evaluationDataLocation + "NA12878.ESP.WEx.chr1.bam" + " -L chr1:1-150,000,000" +